SARS-CoV-2 Lineage Variant Summary

Nucleotide variants related to lineages of concern and observed in > 10% of sequences are indicated in yellow above a schematic SARS-CoV-2 genome. Primers that do not overlap with variants associated with these lineages are shown in blue. Overlapping primers are indicated in orange.

Overlapping amplicons:

Orf1 Gene (1.5 kb) Variants

Orf1 Gene (6 kb) Variants

Orf1 Gene (12 kb) Variants

Orf1 Gene (17 kb) Variants

S Gene Variants

Orf7-N Gene Variants


Sequences reported in Sequence Sources for each lineage were aligned to the NC_045512.2 reference sequence (minimap2). Variants > 10% frequency (freebayes) were evaluated for overlap with primer regions (bedtools) and displayed (Geneious Prime 2021.0.3).

Sequence Sources:

B.1.617.2: GitHub. “Potential Sequences That Should Be Included in B.1.617 · Issue #49 · Cov-Lineages/Pango-Designation.” Accessed June 20, 2021.

AY.1: GitHub. “Proposal for New Sub-Lineage of AY with C5239T and T5514C (ORF1ab:V1750A) in Japan · Issue #208 · Cov-Lineages/Pango-Designation.” Accessed October 1, 2021.

AY.4, AY.5, AY.6: GitHub. “Proposal for Sub-Lineages within B.1.617.2 · Issue #180 · Cov-Lineages/Pango-Designation.” Accessed October 1, 2021.

AY.25: GitHub. “B.1.617.2 Sublineage with Expansion in Cape Cod, Massachusetts, USA in July 2021 · Issue #181 · Cov-Lineages/Pango-Designation.” Accessed October 1, 2021.

Amplicon Designs:

US CDC: Lu, Xiaoyan, Lijuan Wang, Senthilkumar K. Sakthivel, Brett Whitaker, Janna Murray, Shifaq Kamili, Brian Lynch, et al. “US CDC Real-Time Reverse Transcription PCR Panel for Detection of Severe Acute Respiratory Syndrome Coronavirus 2 - Volume 26, Number 8—August 2020 - Emerging Infectious Diseases Journal - CDC.” Accessed April 23, 2021.

China CDC: “新型冠状病毒核酸检测引物和探针序列(Specific Primers and Probes for Detection 2019 Novel Coronavirus).” Accessed June 20, 2021.

Charité: Corman, Victor M., Olfert Landt, Marco Kaiser, Richard Molenkamp, Adam Meijer, Daniel KW Chu, Tobias Bleicker, et al. “Detection of 2019 Novel Coronavirus (2019-NCoV) by Real-Time RT-PCR.” Eurosurveillance 25, no. 3 (January 23, 2020): 2000045.

ARTIC v3: Tyson, John R., Phillip James, David Stoddart, Natalie Sparks, Arthur Wickenhagen, Grant Hall, Ji Hyun Choi, et al. “Improvements to the ARTIC Multiplex PCR Method for SARS-CoV-2 Genome Sequencing Using Nanopore.” BioRxiv: The Preprint Server for Biology, September 4, 2020.

Midnight 1200 bp: Freed, Nikki E., Markéta Vlková, Muhammad B. Faisal, and Olin K. Silander. “Rapid and Inexpensive Whole-Genome Sequencing of SARS-CoV-2 Using 1200 Bp Tiled Amplicons and Oxford Nanopore Rapid Barcoding.” Biology Methods & Protocols 5, no. 1 (2020): bpaa014.

ARTIC v4: ARTIC Real-time Genomic Surveillance. “SARS-CoV-2 Version 4 Scheme Release - Laboratory,” June 24, 2021.

VarSkip: VarSkip Multiplex PCR Designs for SARS-CoV-2 Sequencing. 2021. Reprint, New England Biolabs Inc., 2021.

Software Tools:

Li, Heng. “Minimap2: Pairwise Alignment for Nucleotide Sequences.” Bioinformatics 34, no. 18 (September 15, 2018): 3094–3100. .

Garrison, Erik, and Gabor Marth. “Haplotype-Based Variant Detection from Short-Read Sequencing.” ArXiv:1207.3907 [q-Bio], July 20, 2012.

Quinlan, Aaron R, and Ira M Hall. “BEDTools: A Flexible Suite of Utilities for Comparing Genomic Features.” Bioinformatics (Oxford, England) 26 (2010): 841–42. .

Geneious version 2021.1 created by Biomatters. Available from


2021-10-07: removed duplicate VarSkip amplicon 61

2021-09-29: Added VarSkip, removed new VBM lineages

2021-06-24: Added ARTICv4

2021-06-20: Updated to currently relevant variants of concerns.